Genomics is a field of active research today. Genetic material obtained from an organism is generally sequenced into a plurality of sequences, called genomic sequences. The genomic sequences may be further analyzed to study the characteristics of the corresponding genome, for example, to identify genes and to study the interaction between the genes constituting the genomic sequences. For obtaining a holistic view of the functioning and survival strategies of a given organism in its associated environment, there is not only a need to study each of the individual genomes in isolation, but also a need to understand the extent and the mode of exchange of genomic information across the genomes of diverse organisms in its environment.
A comparative analysis of the genomes of diverse organisms in the same environmental sample has revealed the presence of genes or gene clusters that show a pattern of inheritance that is different from the established phylogenetic tree of life. These genes or gene clusters show a higher sequence homology to genes originating from organisms belonging to different taxonomic clades, than to its close phylogenetic relatives. These genes or gene clusters are observed to be shared across organisms which inhabit the same micro-environment (i.e. physical proximity) rather than the phylogenetic closeness between these organisms. Such physical proximity of different organisms within the same micro-environment increases the chances of exchange of genetic material across diverse species.
The process of exchanging genomic material as a result of which an organism incorporates part of the genetic material from another organism is known as horizontal gene transfer or lateral gene transfer. Such gene-transfer events allow large regions of foreign DNA (Deoxyribonucleic Acid) from ‘donor’ genome to be inserted into the native ‘recipient’ genome and are generally observed to have an oligonucleotide usage pattern distinct from that of the native recipient genome. These exchanged genes or gene-clusters are referred to as horizontally transferred genes or HGT regions.
The horizontally transferred genes confer a selective advantage to the organisms in terms of their growth and survival in the given environment. For instance, such genes or gene-clusters may confer various characteristics, such as resistance against multitude of antibiotics (for example, multidrug resistance gene operons), virulence associated functions comprising secretion machineries (for example, Type III, Type IV, Type VI secretion machineries), and specialized machineries providing defense mechanisms against host immune response in pathogenic organisms. These also include genes that facilitate chemotaxis and adhesion of recipient bacteria to host cell membranes and even those encoding specialized metabolic enzymes that increase the survival chances of the recipient organisms in nutrient-deficient environments.
Thus, efficient detection of such HGT regions in genomes of different organisms provide useful insights in understanding the probable mechanisms of transfer of such genes and in identifying the specific functions that enhance the survival of the recipient organisms in diverse micro-environments.